Isolation and culture of Methanobrevibacter smithii by co-culture with hydrogen-producing bacteria on agar plates

Personalized and precise functional assessment of innovative flatbreads toward the colon microbiota of people with metabolic syndrome: Results from an in vitro simulation

Due to the increasing incidence of individuals with metabolic syndrome and the higher correlations between metabolic syndrome and the gut microbiota, there is a need to formulate functional foods that can promote the development of beneficial microorganisms within the gut microbiota. This study aims to evaluate the possible positive effects of innovative gluten-free flatbread, containing grape and apple antioxidant-rich by-products, on the gut microbiota of patients with metabolic syndrome. The baked products were subjected to gastric digestion using the Infogest system, followed by proximal colonic fermentation in the MICODE (Multi-Unit In vitro Colon Model) intestinal model, where three samplings were performed (baseline, after 16 h and 24 h). The samples were then subjected to 16S rRNA metataxonomy, quantification of shifts in bacterial populations by qPCR analysis and characterization of volatile organic compounds by SPME GC-MS (Solid Phase Micro Extraction Gas-Chromatography Mass-Spectrophotometry). A robust statistical approach based on several tests and multivariate analysis was applied. The results obtained demonstrated the in vitro potential of functional flatbreads in improving the dysbiosis of the microbiota of individuals with metabolic syndrome, due to a reduction in the Firmicutes/Bacteroidota ratio, and highlighted an increase in commensal microorganisms (Bifidobacterium, positive clostridia and Akkermansia muciniphila) and a reduction in negative microorganisms (Enterobacteriaceae, negative clostridia and Collinsella spp.). The analysis of metabolites showed an increase in health-beneficial metabolites (acetate and medium chain organic acids) and a reduction in harmful metabolites (p-cresol and skatole), the degree of this modulation varied based on the flatbread composition. While this study employed an in vitro model of recognized limitations, it nonetheless provides valuable, evidence-based results that can be used for preclinical screening of formulations. Anyhow this work is of high fashion in this running time as it proposes i) in vitro models rather than animal testing; ii) human MetS gut microbiota for high translatability to in vivo condition; iii) approaches of precise and personalized nutrition by the use of specific microbiota and omic technologies, all component that vow to be the future of food assessment.

Poly(p-Phenyleneethynylene)s-Based Sensor Array for Diagnosis of Clinical Diseases

Inspired by the mammalian taste and olfactory systems, array-based pattern recognition technology has demonstrated significant potential in discerning subtle differences between highly similar compounds and complex mixtures, owing to their unique parallel detection mechanism based on cross-reactive signals. While optical sensor array has been extensively employed in the field of chemical sensing, they encounter significant challenges in non-specific recognition of multiple analytes at low concentrations, particularly in rife environments with complex interferences. Poly(p-phenylene ethynylene)s (PPEs) offer substantial advantages in detecting multi-analytes at low concentrations, owing to its distinctive optical properties, including the "molecular wire" effect, fluorescence super-amplification and super-quenching. This is particularly promising for the parallel detection of ultra-low concentration multi-biomarkers in clinical diseases. As the continuous development of PPEs sensor array, more sensitive methods for rapid detection of clinical disease will be further developed. It will promote the further development of the field of early diagnosis of clinical diseases.

Influence of menstrual cycle and oral contraception on taxonomic composition and gas production in the gut microbiome

Introduction. Oral contraceptives (OCs) are widely used for birth control and offer benefits such as menstrual cycle regulation and reduced menstrual pain. However, they have also been associated with an increased risk of cancer and reduced bone mass density.Gap Statement. While the gut microbiome is known to interact with endocrine factors, the impact of hormonal OCs on its composition and function remains underexplored. Additionally, we explore the relationship of OC use and the microbiome to gas production, which can cause symptoms and be indicative of poor health.Aim. This study investigates the effects of OCs on the diversity and composition of the gut microbiome and its association with breath hydrogen (H2) and methane (CH4) levels.Methodology. We utilized 16S rRNA gene sequencing to analyse faecal samples from 65 women, comparing OC users with non-users at two menstrual cycle time points. Breath tests measured hydrogen and CH4 production. Data were analysed for microbial diversity, community composition and correlation with gas production.Results. There were no differences in overall microbial diversity between OC users and non-users in samples collected on day 2 of the menstrual cycle. However, on day 21, we found a significant difference in microbial richness, suggesting a cycle-dependent effect of OCs on gut microbiota species richness but not composition. We found a strong correlation between H2 and CH4 concentrations and an interaction between OC use and the menstrual cycle on H2 and CH4 production. We also identified several taxa associated with both high levels of H2 and CH4 production and OC use.Conclusion. Our study highlights the intricate relationships among hormonal contraceptives, the gut microbiota and gas production and connects shifts in the microbiome composition to gastrointestinal symptoms (e.g. gas production) that can impact overall health. This underscores the need for further research on the long-term effects of OCs and for the development of precise therapeutic strategies to address potential adverse effects. Our findings offer new perspectives on the microbiome-hormone-gas production nexus, potentially broadening our understanding of the systemic implications of OCs.

Methanobrevibacter smithii cell variants in human physiology and pathology: A review

Methanobrevibacter smithii (M. smithii), initially isolated from human feces, has been recognised as a distinct taxon within the Archaea domain following comprehensive phenotypic, genetic, and genomic analyses confirming its uniqueness among methanogens. Its diversity, encompassing 15 genotypes, mirrors that of biotic and host-associated ecosystems in which M. smithii plays a crucial role in detoxifying hydrogen from bacterial fermentations, converting it into mechanically expelled gaseous methane. In microbiota in contact with host epithelial mucosae, M. smithii centres metabolism-driven microbial networks with Bacteroides, Prevotella, Ruminococcus, Veillonella, Enterococcus, Escherichia, Enterobacter, Klebsiella, whereas symbiotic association with the nanoarchaea Candidatus Nanopusillus phoceensis determines small and large cell variants of M. smithii. The former translocate with bacteria to induce detectable inflammatory and serological responses and are co-cultured from blood, urine, and tissular abscesses with bacteria, prototyping M. smithii as a model organism for pathogenicity by association. The sources, mechanisms and dynamics of in utero and lifespan M. smithii acquisition, its diversity, and its susceptibility to molecules of environmental, veterinary, and medical interest still have to be deeply investigated, as only four strains of M. smithii are available in microbial collections, despite the pivotal role this neglected microorganism plays in microbiota physiology and pathologies.

Bacterial Insights: Unraveling the Ocular Microbiome in Glaucoma Pathogenesis

This review explores the connection between the ocular surface microbiome and glaucoma, highlighting its impact on disease progression. Beginning with an overview of global glaucoma significance, it emphasizes the importance of understanding the cellular characteristics and microbiology of the ocular microbiome. A search was conducted on the PubMed and Cochrane Library databases using the phrase "ocular microbiome glaucoma". 0 records were returned from the Cochrane Library while 21 were returned from PubMed. A total of 21 results were retrieved from 2017 to 2024. This comprised one opinion paper, four original research articles, and 16 reviews. This review covered the anatomy of the ocular surface, advanced analysis methods, and the ocular microbiome. It also delved into dysbiosis in glaucoma, addressing altered microbial communities and their potential role in disease progression. The intricate interplay between the ocular microbiome and the host's immune system is explored, emphasizing crosstalk and inflammatory responses. The review concludes by discussing therapeutic implications, including modulating ocular microbiota and potential future treatment strategies. Understanding the microbiome in healthy and glaucomatous eyes can help researchers and clinicians in innovative approaches to ocular health.

Food-borne bacteria analysis using a diatomite bioinspired SERS platform

Rapid and sensitive detection of food-borne bacteria has remained challenging over the past few decades. We propose a surface-enhanced Raman scattering sensing strategy based on a novel bioinspired surface-enhanced Raman scattering substrate, which can directly detect dye molecular residues and food-borne pathogen microorganisms in the environment. The surface-enhanced Raman scattering platform consists of a natural diatomite microporous array decorated with a metal-phenolic network that enables the in situ reduction of gold nanoparticles. The as-prepared nanocomposites display excellent surface-enhanced Raman scattering activity with the lowest limit of detection and the maximum Raman enhancement factor of dye molecules up to 10-11 M and 1.18 × 107, respectively. For food-borne bacterial detection, a diatomite microporous array decorated with a metal polyphenol network and gold nanoparticle-based surface-enhanced Raman scattering analysis is capable of distinguishing the biochemical fingerprint information of Staphylococcus aureus and Escherichia coli, indicating the great potential for strain identification.

Thermal hydrolysis alleviates polyethylene microplastic-induced stress in anaerobic digestion of waste activated sludge

Microplastics are known to negatively affect anaerobic digestion (AD) of waste activated sludge. However, whether thermal hydrolysis (TH) pretreatment alters the impact of microplastics on sludge AD remains unknown. Herein, the effect of TH on the impact of polyethylene (PE) microplastics in sludge AD was investigated. The results showed that the inhibition of methane production by PE at 100 particles/g total solids (TS) was reduced by 31.4% from 12.1% to 8.3% after TH at 170 °C for 30 min. Mechanism analysis indicated TH reduced the potential for reactive oxygen species production induced by PE, resulting in a 29.1 ± 5.5% reduction in cell viability loss. In addition, additive leaching increased as a result of rapid aging of PE microplastics by TH. Acetyl tri-n-butyl citrate (ATBC) release from PE with 10 and 100 particles/g TS increased 11.5-fold and 8.6-fold after TH to 68.2 ± 5.5 μg/L and 124.0 ± 5.1 μg/L, respectively. ATBC at 124.0 μg/L increased methane production by 21.4%. The released ATBC enriched SBR1031 and Euryarchaeota, which facilitate the degradation of proteins and promote methane production. This study reveals the overestimated impact of PE microplastics in sludge AD and provides new insights into the PE microplastics-induced impact in practical sludge treatment and anaerobic biological processes.

A Dual Fluorescence Turn-On Sensor Array Formed by Poly(para-aryleneethynylene) and Aggregation-Induced Emission Fluorophores for Sensitive Multiplexed Bacterial Recognition

Bacterial infections have emerged as the leading causes of mortality and morbidity worldwide. Herein, we developed a dual-channel fluorescence "turn-on" sensor array, comprising six electrostatic complexes formed from one negatively charged poly(para-aryleneethynylene) (PPE) and six positively charged aggregation-induced emission (AIE) fluorophores. The 6-element array enabled the simultaneous identification of 20 bacteria (OD600=0.005) within 30s (99.0 % accuracy), demonstrating significant advantages over the array constituted by the 7 separate elements that constitute the complexes. Meanwhile, the array realized different mixing ratios and quantitative detection of prevalent bacteria associated with urinary tract infection (UTI). It also excelled in distinguishing six simulated bacteria samples in artificial urine. Remarkably, the limit of detection for E. coli and E. faecalis was notably low, at 0.000295 and 0.000329 (OD600), respectively. Finally, optimized by diverse machine learning algorithms, the designed array achieved 96.7 % accuracy in differentiating UTI clinical samples from healthy individuals using a random forest model, demonstrating the great potential for medical diagnostic applications.

Sourdough process and spirulina-enrichment can mitigate the limitations of colon fermentation performances of gluten-free breads in non-celiac gut model

In this work, the impact of gluten free (GF) breads enriched with spirulina on the ecology of the colon microbiota of non-celiac volunteers was investigated. Simulation of digestion of GF breads was conducted with an in vitro gut model. Microbiomics and metabolomics analyses were done during colon fermentations to study the modulation of the microbiota. From the results, a general increase in Proteobacteria and no reduction of detrimental microbial metabolites were observed in any conditions. Notwithstanding, algae enriched sourdough breads showed potential functionalities, as the improvement of some health-related ecological indicators, like i) microbiota eubiosis; ii) production of bioactive volatile organic fatty acids; iii) production of bioactives terpenes. Our results indicate that a sourdough fermentation and algae enrichment can mitigate the negative effect of GF breads on gut microbiota of non-celiac consumers.

Carbon dioxide and trace oxygen concentrations impact growth and product formation of the gut bacterium Phocaeicola vulgatus

BACKGROUND

The promising yet barely investigated anaerobic species Phocaeicola vulgatus (formerly Bacteroides vulgatus) plays a vital role for human gut health and effectively produces organic acids. Among them is succinate, a building block for high-value-added chemicals. Cultivating anaerobic bacteria is challenging, and a detailed understanding of P. vulgatus growth and metabolism is required to improve succinate production. One significant aspect is the influence of different gas concentrations. CO2 is required for the growth of P. vulgatus. However, it is a greenhouse gas that should not be wasted. Another highly interesting aspect is the sensitivity of P. vulgatus towards O2. In this work, the effects of varying concentrations of both gases were studied in the in-house developed Respiratory Activity MOnitoring System (RAMOS), which provides online monitoring of CO2, O2, and pressure under gassed conditions. The RAMOS was combined with a gas mixing system to test CO2 and O2 concentrations in a range of 0.25-15.0 vol% and 0.0-2.5 vol%, respectively.

RESULTS

Changing the CO2 concentration in the gas supply revealed a CO2 optimum of 3.0 vol% for total organic acid production and 15.0 vol% for succinate production. It was demonstrated that the organic acid composition changed depending on the CO2 concentration. Furthermore, unrestricted growth of P. vulgatus up to an O2 concentration of 0.7 vol% in the gas supply was proven. The viability decreased rapidly at concentrations larger than or equal to 1.3 vol% O2.

CONCLUSIONS

The study showed that P. vulgatus requires little CO2, has a distinct O2 tolerance and is therefore well suited for industrial applications.

In vitro interactions between Blautia hydrogenotrophica, Desulfovibrio piger and Methanobrevibacter smithii under hydrogenotrophic conditions

Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each other remains largely unknown. This in vitro study cocultured Blautia hydrogenotrophica (reductive acetogen), Desulfovibrio piger (sulfate reducer) and Methanobrevibacter smithii (methanogen). Results revealed that these three species coexisted and did not compete for hydrogen in the early phase of incubations. Sulfate reduction was not affected by B. hydrogenotrophica and M. smithii. D. piger inhibited the growth of B. hydrogenotrophica and M. smithii after 10 h incubations, and the inhibition on M. smithii was associated with increased sulfide concentration. Remarkably, M. smithii growth lag phase was shortened by coculturing with B. hydrogenotrophica and D. piger. Formate was rapidly used by M. smithii under high acetate concentration. Overall, these findings indicated that the interactions of the hydrogenotrophic microbes are condition-dependent, suggesting their interactions may vary in gut ecosystems.

High extinction coefficient material combined with multi-line lateral flow immunoassay strip for ultrasensitive detection of bacteria

Lateral flow immunoassay strips (LFIAs) are a reliable and point-of-care detection method for rapid monitoring of bacteria, but their sensitivity was limited by the low extinction coefficient of colloidal gold nanoparticles (Au NPs) and low capture efficiency of test-line. In this study, polydopamine nanoparticles (PDA NPs) were employed to replace Au NPs, due to their high extinction coefficient. And the amount of test-line was increased to 5 for further improving the efficiency of bacteria capture. Thus, under visual observation, the detection limits of PDA-based LFIAs (102 CFU/mL) were about 2 orders of magnitude lower than Au-based LFIAs (104 CFU/mL). Furthermore, the invisible signal could be collected by Image J and the detection limit can reach 10 CFU/mL. The proposed test strips were successfully applied for the quantitative, accurate, and rapid screening of E. coli in food samples. This study provided a universal approach to enhance the sensitivity of bacteria LFIAs.

A magnetic field augmented ultra-thin layer chromatography coupled surface enhanced Raman spectroscopy separation of hemozoin from bacterial mixture

Malaria is considered as one the most widespread disease with highest possibility of co-infection at all levels of the disease prognosis. Rapid detection and discrimination of malaria from other co-infections remains a challenge. Hemozoin is a metabolic biproduct of malaraia possessing paramagnetic property due to presence of iron at its centre. Here, we report a label free, rapid and highly sensitive magnetic field based ultra-thin layer chromatography (UTLC) coupled with surface enhanced Raman spectroscopy (SERS) technique for detection and separation of hemozoin from a bacterial mixture. Highly optimized silver nanorods chip fabricated using glancing angle deposition (GLAD) is explored for the UTLC-SERS separation. These chips possessing channel like characteristic and high surface to the volume ratio serve as excellent UTLC plates. The magnetic nature of hemozoin has been exploited for its separation from the mixture of P. aeruginosa (Gram-negative) and S. aureus (Gram-positive) by allocating a 0.6 T magnet over the UTLC flow setup. The solvent front migrated approximately to a distance of 13 mm from the sample point due to the magnetic environment. Spatially resolved SERS data was collected along the mobile phase and separation of mixture was confirmed. Further, staining of hemozoin, P. aeruginosa and S. aureus was done using methylene blue, acridine orange and rhodamine 6 G respectively. The separation was confirmed for the stained analytes. The present developed method provides plate height as low as 18 µm and hemozoin detection limit as <10 parasites/mL. Therefore, we establish a highly specific and sensitive technique capable of separating small amounts of bioanalytes, aiding in the removal of co-infections from the disease at a very early stage of infection.

Hydrogen online monitoring based on thermal conductivity for anaerobic microorganisms

H₂ -producing microorganisms are a promising source of sustainable biohydrogen. However, most H₂ -producing microorganisms are anaerobes, which are difficult to cultivate and characterize. While several methods for measuring H₂ exist, common H₂ sensors often require oxygen, making them unsuitable for anaerobic processes. Other sensors can often not be operated at high gas humidity. Thus, we applied thermal conductivity (TC) sensors and developed a parallelized, online H₂ monitoring for time-efficient characterization of H₂ production by anaerobes. Since TC sensors are nonspecific for H₂ , the cross-sensitivity of the sensors was evaluated regarding temperature, gas humidity, and CO₂ concentrations. The systems' measurement range was validated with two anaerobes: a high H₂ -producer (Clostridium pasteurianum) and a low H₂ -producer (Phocaeicola vulgatus). Online monitoring of H₂ production in shake flask cultivations was demonstrated, and H₂ transfer rates were derived. Combined with online CO₂ and pressure measurements, molar gas balances of the cultivations were closed, and an anaerobic respiration quotient was calculated. Thus, insight into the effect of medium components and inhibitory cultivation conditions on H₂ production with the model anaerobes was gained. The presented online H₂ monitoring method can accelerate the characterization of anaerobes for biohydrogen production and reveal metabolic changes without expensive equipment and offline analysis.

Isolation and Cultivation of Human Gut Microorganisms: A Review

Microbial resources from the human gut may find use in various applications, such as empirical research on the microbiome, the development of probiotic products, and bacteriotherapy. Due to the development of "culturomics", the number of pure bacterial cultures obtained from the human gut has significantly increased since 2012. However, there is still a considerable number of human gut microbes to be isolated and cultured. Thus, to improve the efficiency of obtaining microbial resources from the human gut, some constraints of the current methods, such as labor burden, culture condition, and microbial targetability, still need to be optimized. Here, we overview the general knowledge and recent development of culturomics for human gut microorganisms. Furthermore, we discuss the optimization of several parts of culturomics including sample collection, sample processing, isolation, and cultivation, which may improve the current strategies.

The Overlooked Microbiome-Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes

In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the relevance of archaea in human health and diseases. Contemporary broad availability and spread of next generation sequencing techniques now enable a stronger focus on such microorganisms, whose cultivation is difficult. However, due to the enormous evolutionary distances between bacteria, archaea and eukaryotes, the implementation of sequencing strategies for smaller laboratory scales needs to be refined to achieve as a holistic view on the microbiome as possible. Here, we present a technical approach that enables simultaneous analyses of archaeal, bacterial and eukaryotic microbial communities to study their roles in development and courses of respiratory disorders. We thus applied combinatorial 16S-/18S-rDNA sequencing strategies for sequencing-library preparation. Considering the lower total microbiota density of airway surfaces, when compared with gut microbiota, we optimized the DNA purification workflow from nasopharyngeal swab specimens. As a result, we provide a protocol that allows the efficient combination of bacterial, archaeal, and eukaryotic libraries for nanopore-sequencing using Oxford Nanopore Technologies MinION devices and subsequent phylogenetic analyses. In a pilot study, this workflow allowed the identification of some environmental archaea, which were not correlated with airway microbial communities before. Moreover, we assessed the protocol's broader applicability using a set of human stool samples. We conclude that the proposed protocol provides a versatile and adaptable tool for combinatorial studies on bacterial, archaeal, and eukaryotic microbiomes on a small laboratory scale.

Cecal Microbial Hydrogen Cycling Potential Is Linked to Feed Efficiency Phenotypes in Chickens

In chickens, early life exposure to environmental microbes has long-lasting impacts on gastrointestinal (GI) microbiome development and host health and growth, via mechanisms that remain uncharacterized. In this study, we demonstrated that administrating a fecal microbiome transplant (FMT) from adults to day-of-hatch chicks results in significantly higher body mass of birds and decreased residual feed intake (RFI), implying enhanced feed efficiency, at 6 weeks of age. To assess the potential mechanisms through which FMT affects adult bird phenotype, we combined 16 S rRNA gene amplification, metagenomic, and comparative genomic approaches to survey the composition and predicted activities of the resident microbiome of various GI tract segments. Early life FMT exposure had a long-lasting significant effect on the microbial community composition and function of the ceca but not on other GI segments. Within the ceca of 6-week-old FMT birds, hydrogenotrophic microbial lineages and genes were most differentially enriched. The results suggest that thermodynamic regulation in the cecum, in this case via hydrogenotrophic methanogenic and sulfur-cycling lineages, potentially serving as hydrogen sinks, may enhance fermentative efficiency and dietary energy harvest capacity. Our study provides a specific mechanism of action through which early-life microbiome transplants modulate market-relevant phenotypes in poultry and, thereby, may represent a significant advance toward microbiome-focused sustainable agriculture.

Archaeal key-residents within the human microbiome: characteristics, interactions and involvement in health and disease

Since the introduction of Archaea as new domain of life more than 40 years ago, they are no longer regarded as eccentric inhabitants of extreme ecosystems. These microorganisms are widespread in various moderate ecosystems, including eukaryotic hosts such as humans. Indeed, members of the archaeal community are now recognized as paramount constituents of human microbiome, while their definite role in disease or health is not fully elucidated and no archaeal pathogen has been reported. Here, we present a brief overview of archaea residing in and on the human body, with a specific focus on common lineages including Methanobrevibacter, Methanosphaeraand Methanomassilococcales.

Cation exchange resin pretreatment enhancing methane production from anaerobic digestion of waste activated sludge

The application of anaerobic digestion (AD) to treat waste activated sludge (WAS) still exhibits some limitations, such as low methane production. In this study, cation exchange resin (CER) pretreatment was explored to enhance the efficiency of the AD of WAS. Based on the response surface methodology, the optimal conditions for CER pretreatment were reaction time of 7.4 h, 33.8 g CER (wet weight) /g volatile solids and sludge total solids of 2.4%. Under these optimal CER pretreatment conditions, approximately 30% of metals were removed from the WAS, particularly organic-binding metals. This metal removal disrupted the structures of extracellular polymer substances and led to sludge deflocculation, thereby releasing large amounts of organic substances from the sludge solids. Batch AD experiments showed that CER pretreatment increased the maximal production of volatile fatty acids and methane by 565.7% and 80.5%, respectively. Additionally, CER pretreatment promoted each stage of AD (i.e. solubilisation, hydrolysis, acidification and methanation) and the corresponding activities of key enzymes. Experimental results for semi-continuous AD further confirmed that CER pretreatment enhanced the proportion of methane in the biogas (from 62.75 ± 2.14% to 73.96 ± 0.99%) and the production of methane. An analysis of changes in the microbial communities demonstrated that CER pretreatment enhanced the abundance of microorganisms involved in hydrolysis, acidification and acetification and changed the major methanogenic pathway from acetoclastic methanogens to methylotrophic methanogens. These findings are expected to provide a reference for developing new pretreatment methods for enhancing anaerobic biodegradability of organic matters.

Highly sensitive and selective antibody microarrays based on a Cy5-antibody complexes coupling ES-biochip for E. coli and Salmonella detection

Foodborne pathogens are threats in food and a cause of major health issues globally. Microbial safety has become a key concern to eliminate disease-causing pathogens from the food supply. For this purpose, the Cy5 dye conjugated with a double-biotin DNA linkage and a detection antibody (Cy5-Ab complexes) was developed to amplify a foodborne detection signal on a microarray. Additionally, the ES-biochip was designed to attain a visual screening of an antibody microarray for the simultaneous threat detection of Salmonella and Escherichia coli (E. coli). Quantification was also performed by fluorescence. After optimizing the Cy5-Ab complex appendage and enhancing the detection signal from a sandwich immunoassay, high sensitivity and selectivity were observed. The limits of detection for both pathogens in buffer and food samples were 10³ CFU mL⁻¹ and less than 9 CFU mL⁻¹ by visual screening and fluorescent intensity quantification, respectively. Mono and duplex responses were not significantly different which means that no cross-reactivity occurred. Uniquely, the assays hold great potential to be used in several fields, such as clinical diagnosis of foodborne microbes, food hygiene screening, and pathogen detection.

A visual ES-biochip was highly sensitive and selective as well as enabled simultaneous detection. An optimized amount of Cy5 dye was attached to a Cy5-Ab complex label using a double-biotin DNA linkage.

Bacteria Detection: From Powerful SERS to Its Advanced Compatible Techniques

The rapid, highly sensitive, and accurate detection of bacteria is the focus of various fields, especially food safety and public health. Surface-enhanced Raman spectroscopy (SERS), with the advantages of being fast, sensitive, and nondestructive, can be used to directly obtain molecular fingerprint information, as well as for the on-line qualitative analysis of multicomponent samples. It has therefore become an effective technique for bacterial detection. Within this progress report, advances in the detection of bacteria using SERS and other compatible techniques are discussed in order to summarize its development in recent years. First, the enhancement principle and mechanism of SERS technology are briefly overviewed. The second part is devoted to a label-free strategy for the detection of bacterial cells and bacterial metabolites. In this section, important considerations that must be made to improve bacterial SERS signals are discussed. Then, the label-based SERS strategy involves the design strategy of SERS tags, the immunomagnetic separation of SERS tags, and the capture of bacteria from solution and dye-labeled SERS primers. In the third part, several novel SERS compatible technologies and applications in clinical and food safety are introduced. In the final part, the results achieved are summarized and future perspectives are proposed.

State of the Art in the Culture of the Human Microbiota: New Interests and Strategies

The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.

Simultaneous Detection of Three Foodborne Pathogens Based on Immunomagnetic Nanoparticles and Fluorescent Quantum Dots

This paper presents a peptide-mediated immunomagnetic separation technique and an immunofluorescence quantum dot technique for simultaneous and rapid detection of Escherichia coli O157:H7, Staphylococcus aureus, and Vibrio parahaemolyticus. First, three peptides that can specifically recognize the three foodborne pathogens were combined with magnetic nanoparticles to form an immunomagnetic nanoparticle probe for capturing three kinds of target bacteria and then added three quantum dot probes (quantum dots-aptamer), which formed a sandwich composite structure. When the three quantum dot probes specifically combined with the three pathogenic bacteria, the remaining fluorescent signal in the supernatant will be reduced by magnetic separation. Therefore, the remaining fluorescent signal in the supernatant can be measured with a fluorescence spectrophotometer to indirectly determine the three pathogens in the sample. The linear range of the method was 10-10⁷ cfu/mL, and in the buffer, the detection limits of E. coli O157:H7, S. aureus, and V. parahaemolyticus were 2.460, 5.407, and 3.770 cfu/mL, respectively. In the tap water simulation, the detection limits of E. coli O157:H7, S. aureus, and V. parahaemolyticus were 2.730, 1.990 × 10¹, and 4.480 cfu/mL, respectively. In the milk simulation sample, the detection limits of E. coli O157:H7, S. aureus, and V. parahaemolyticus were 6.660, 1.070 × 10¹, and 2.236 × 10¹ cfu/mL, respectively. The method we presented can detect three kinds of foodborne pathogens at the same time, and the entire experimental process did not exceed 4 h. It has high sensitivity and low detection limit and may be used in the sample detection of other pathogens.

Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases

Archaea, which form one of four domains of life alongside Eukarya, Bacteria, and giant viruses, have long been neglected as components of the human microbiota and potential opportunistic infectious pathogens. In this review, we focus on methanogenic Archaea, which rely on hydrogen for their metabolism and growth. On one hand, methanogenic Archaea in the gut are functional associates of the fermentative digestion of dietary fibers, favoring the production of beneficial short-chain fatty acids and likely contributing to the weaning reaction during the neonatal window of opportunity. On the other hand, methanogenic Archaea trigger the activation of innate and adaptive responses and the generation of specific T and B cells in animals and humans. In mouse models, lung hypersensitivity reactions can be induced by inhaled methanogenic Archaea mimicking human professional exposure to organic dust. Changes in methanogenic Archaea of the microbiota are detected in an array of dysimmune conditions comprising inflammatory bowel disease, obesity, malnutrition, anorexia, colorectal cancer, and diverticulosis. At the subcellular level, methanogenic Archaea are activators of the TLR8-dependent NLRP3 inflammasome, modulate the release of antimicrobial peptides and drive the production of proinflammatory, Th-1, Th-2, and Th-17 cytokines. Our objective was to introduce the most recent and major pieces of evidence supporting the involvement of Archaea in the balance between health and dysimmune diseases, with a particular focus on atopic and allergic conditions.

Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut

Across human populations, 16S rRNA gene-based surveys of gut microbiomes have revealed that the bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae cooccur and are enriched in individuals with a lean, compared to an obese, body mass index (BMI). Whether these association patterns reflect interactions between metabolic partners, as well as whether these associations play a role in the lean host phenotype with which they associate, remains to be ascertained. Here, we validated previously reported cooccurrence patterns of the two families and their association with a lean BMI with a meta-analysis of 1,821 metagenomes derived from 10 independent studies. Furthermore, we report positive associations at the genus and species levels between Christensenella spp. and Methanobrevibacter smithii, the most abundant methanogen of the human gut. By coculturing three Christensenella spp. with M. smithii, we show that Christensenella spp. efficiently support the metabolism of M. smithii via H₂ production far better than Bacteroides thetaiotaomicron does. Christensenella minuta forms flocs colonized by M. smithii even when H₂ is in excess. In culture with C. minuta, H₂ consumption by M. smithii shifts the metabolic output of C. minuta's fermentation toward acetate rather than butyrate. Together, these results indicate that the widespread cooccurrence of these microorganisms is underpinned by both physical and metabolic interactions. Their combined metabolic activity may provide insights into their association with a lean host BMI.IMPORTANCE The human gut microbiome is made of trillions of microbial cells, most of which are Bacteria, with a subset of Archaea The bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae are widespread in human guts. They correlate with each other and with a lean body type. Whether species of these two families interact and how they affect the body type are unanswered questions. Here, we show that species within these families correlate with each other across people. We also demonstrate that particular species of these two families grow together in dense flocs, wherein the bacteria provide hydrogen gas to the archaea, which then make methane. When the archaea are present, the ratio of bacterial products (which are nutrients for humans) is changed. These observations indicate that when these species grow together, their products have the potential to affect the physiology of their human host.

Biogas Production from Oil Palm Empty Fruit Bunches and Palm Oil Decanter Cake using Solid-State Anaerobic co-Digestion

Oil palm empty fruit bunches (EFB) and palm oil decanter cake (DC) were used to investigate biogas production by using solid-state anaerobic co-digestion (SS-AcoD) with 15% total solid (TS) content. Solid state anaerobic digestion (SS-AD) using substrate to inoculum (S:I) ratio of 3:1, methane yields of 353.0 mL-CH4/g-VS and 101.5 mL-CH4/g-VS were respectively achieved from mono-digestion of EFB without oil palm ash (OPA) addition and of DC with 10% OPA addition under mesophilic conditions 35 °C. By adding 5% OPA to SS-AD using 3:1 S:I ratio under thermophilic conditions (55 °C), mono-digestion of EFB and DC provided methane yields of 365.0 and 160.3 mL-CH4/g-VS, respectively. Furthermore, SS-AcoD of EFB:DC at 1:1 mixing ratio (volatile solid, VS basis), corresponding to carbon to nitrogen (C:N) ratio of 32, gathering with S:I ratio of 3:1 and 5% ash addition, synergistic effect is observed together with similar methane yields of 414.4 and 399.3 mL-CH4/g-VS, achieved under 35 °C and 55 °C, respectively. According to first order kinetic analysis under synergistic condition, methane production rate from thermophilic operation is 5 times higher than that from mesophilic operation. Therefore, SS-AcoD could be potentially beneficial to generate biogas from EFB and DC.

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson’s index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium. In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii. In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.